Hi thePalindrome! I would love to adjust those as soon as I can replicate your issue. I tried re-downloading both versions (dotnet and notdotnet) from itch.io (to be sure), and extracting it with the native Windows 11 file explorer and with 7zip. In each case, I was able to run the game and have all files seemingly at the proper location. Can you give me more details on your repro steps?
Also, I want to make sure I understand your description. When you unzip, specifically for the example you gave, the "ButtonParagraph-Default.xnb" file is unzipped in the current top folder (so next to HardChip.exe) instead of in a subfolder (precisely "Content\GeonBit.UI\themes\editor\styles\"). Did I get your issue right?
notes: you are right. The build process uses the PowerShell built-in cmd line to zip the game, which seems to be the same as the file explorer one.